"Ko proved to be more comfortable communicating with the Russian cosmonauts and he scored higher on performance and scientific experiment tests," Chung said.
"We would like to make clear that the decision can be overturned should the selected astronaut at any time be deemed unsuited to fulfil the mission," Chung said.
Ko, who has a degree in mathematics from elite Seoul National University, will work on the International Space Station for about 10 days with two Russian cosmonauts in April, conducting scientific experiments.
Neither Ko nor Yi were present at the announcement as both were in Russia for training.
"I am so happy this very moment and thank you,'' Ko said in a statement
issued by the ministry.
South Korea is scheduled to complete the country's first space centre in Goheung, about 470km south of Seoul, by the end of next year, a move aimed at laying technological and scientific groundwork for eventual space exploration.
Ko's mission next year will make South Korea the world's 35th country and Asia's sixth to send an astronaut into space.
Malaysia is due shortly to announce the name of its first astronaut.
One of two Malaysians currently being trained at the Russia's Star City training center will be blasted into space on October 10.